There was no ceremony for the departure from Schiphol airport, local news agency ANP reported, with the plane to land in Malaysia on Friday, which has been declared a day of national mourning.
The plane will be met by Malaysia's king, prime minister and other dignitaries accompanied by a minute of silence at Kuala Lumpur's main international airport, Deputy Prime Minister Muhyiddin Yassin said last week.
The remains will then be taken to the hometowns of the victims' next-of-kin to be laid to rest.
The Malaysia Airlines plane was shot down over rebel-held eastern Ukraine on July 17 en route from Amsterdam to Kuala Lumpur, killing all 298 on board.
More than 220 coffins filled with remains have been taken to the Netherlands for identification.
Of those aboard, 193 were Dutch and 43 were Malaysians, including 15 crew members.
A total of 28 Malaysian victims have been identified in the Netherlands, which is in charge of the identification process.
Some victims may never be identified after the search for body parts was called off at the crash site because of ongoing fighting between Ukrainian forces and pro-Russian separatists.